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arc85 / singleseqgset

Gene set enrichment analysis for single-cell RNAseq data
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Genes in enriched pathways #2

Open ziyan109 opened 4 years ago

ziyan109 commented 4 years ago

Hello,

This is such a great tool and I was able to generate the heatmap :) I'm wondering is there any function to pull out the genes that are enriched in certain pathway? For example, TGF-beta signaling pathway is enriched in one of my clusters, I wonder which genes are up-regulated in there.

Thanks so much.

arc85 commented 2 years ago

Hi Ziyan, great point. It would be helpful to explore "leading edge" genes directly from this package.

abedkurdi commented 1 year ago

Excuse me, but where to find the function related to "leading edge"?

ziyan109 commented 1 year ago

Hi, I was referring to the "leading edge gene" returned by the fgsea package. Is it possible to do it in singleseqgset?

Thanks!

On Thu, Jan 5, 2023 at 11:15 AM Abdullah El Kurdi @.***> wrote:

Excuse me, but where to find the function related to "leading edge"?

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abedkurdi commented 1 year ago

Yeah, I guess, but no idea how. I will give it a try when I have some time.